diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 4a8fe7f1c55b58253c2dddc5406f519bccfffb0d..d6f6aa0e6036b383d65d9519a3c4b0a6d3176835 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -69,6 +69,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningQue
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ExperimentFeatureVectorSummaryLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.FeatureVectorValuesLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.LogicalImageLoader;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.MaterialAllAssaysFeatureVectorSummaryLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.MaterialFeatureVectorSummaryLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningApiImpl;
@@ -313,8 +314,8 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
Session session = getSession(sessionToken);
// NOTE: we want the settings to be passed form the client in future
MaterialSummarySettings settings = createDefaultSettings();
- return MaterialFeatureVectorSummaryLoader.loadMaterialFeatureVectorsFromAllAssays(session,
- businessObjectFactory, getDAOFactory(), materialId, settings);
+ return MaterialAllAssaysFeatureVectorSummaryLoader.loadMaterialFeatureVectorsFromAllAssays(
+ session, businessObjectFactory, getDAOFactory(), materialId, settings);
}
public static MaterialSummarySettings createDefaultSettings()
@@ -469,5 +470,4 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return MINOR_VERSION;
}
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
index 0ad99b5018a3abcd5d618eec1008f8feb43e8cc3..c337dd81e44dc616f778bfee379b10b2a7642974 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ExperimentFeatureVectorSummaryLoader.java
@@ -27,7 +27,6 @@ import java.util.Set;
import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.collections.CollectionUtils.ICollectionMappingFunction;
-import ch.systemsx.cisd.common.collections.GroupByMap;
import ch.systemsx.cisd.common.collections.IKeyExtractor;
import ch.systemsx.cisd.common.collections.TableMap;
import ch.systemsx.cisd.common.collections.TableMap.UniqueKeyViolationStrategy;
@@ -36,7 +35,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleL
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
@@ -46,20 +44,17 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObject
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellExtendedData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellDataCollection;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorValues;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSFeatureVectorLoader;
/**
* {@See #loadExperimentFeatureVectors}.
@@ -114,7 +109,7 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
return enrichWithMaterial(summaries, wellDataCollection);
}
- protected final List<MaterialIdFeatureVectorSummary> calculateReplicasFeatureVectorSummaries(
+ private final List<MaterialIdFeatureVectorSummary> calculateReplicasFeatureVectorSummaries(
List<? extends IWellData> wellDataList)
{
return WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(wellDataList,
@@ -189,6 +184,13 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
featureVectorsCollection.getFeatureCodesAndLabels());
}
+ private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
+ Set<PlateIdentifier> plateIdentifiers)
+ {
+ return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory)
+ .tryLoadWellSingleFeatureVectors(plateIdentifiers, settings.getFeatureCodes());
+ }
+
private static ExperimentFeatureVectorSummary createEmptySummary(ExperimentReference experiment)
{
List<MaterialFeatureVectorSummary> materialsSummary = Collections.emptyList();
@@ -262,7 +264,8 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
{
return null;
}
- return new WellData(replicaMaterial.getId(), featureVectorNumbers, well, replicaMaterial);
+ return new WellExtendedData(replicaMaterial.getId(), featureVectorNumbers, well,
+ replicaMaterial);
}
private static Material tryFindReplicaMaterial(Sample well, MaterialSummarySettings settings)
@@ -292,26 +295,8 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
{
return null;
}
- return asFeatureVectorValues(featureVector, orderedFeatureLabels);
- }
-
- private static float[] asFeatureVectorValues(FeatureVectorValues featureVector,
- List<String> orderedFeatureLabels)
- {
- Map<String, FeatureValue> featureMap = featureVector.getFeatureMap();
- float[] values = new float[featureMap.size()];
- int i = 0;
- for (String featureLabel : orderedFeatureLabels)
- {
- FeatureValue featureValue = featureMap.get(featureLabel);
- values[i++] = asFloat(featureValue);
- }
- return values;
- }
-
- private static float asFloat(FeatureValue featureValue)
- {
- return featureValue.isFloat() ? featureValue.asFloat() : Float.NaN;
+ return WellFeatureCollectionLoader.asFeatureVectorValues(featureVector,
+ orderedFeatureLabels);
}
private static WellReference asWellReference(Sample well)
@@ -332,32 +317,6 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
return idents;
}
- // private static List<WellContent> convert(List<Sample> wells, ExperimentReference experiment)
- // {
- // List<WellContent> wellContents = new ArrayList<WellContent>();
- // for (Sample well : wells)
- // {
- // wellContents.add(convert(well, experiment));
- // }
- // return wellContents;
- // }
- //
- // private static WellContent convert(Sample well, ExperimentReference experiment)
- // {
- // WellLocation location =
- // ScreeningUtils.tryCreateLocationFromMatrixCoordinate(well.getSubCode());
- // EntityReference wellReference = asEntityReference(well);
- // EntityReference plate = asEntityReference(well.getContainer());
- //
- // return new WellContent(location, wellReference, plate, experiment);
- // }
- //
- // private static EntityReference asEntityReference(Sample sample)
- // {
- // return new EntityReference(sample.getId(), sample.getSubCode(), sample.getSampleType()
- // .getCode(), EntityKind.SAMPLE, sample.getPermId());
- // }
-
private static ListOrSearchSampleCriteria createWellsCriteria(List<Sample> plates)
{
Collection<Long> plateIds = new ArrayList<Long>();
@@ -377,112 +336,6 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
ListOrSearchSampleCriteria.createForExperiment(new TechId(expId)));
}
- /**
- * Fetches feature vectors from different datastores and merges them (assuming that feature
- * codes are the same).
- */
- private static class FeatureVectorRetriever
- {
- public static WellFeatureCollection<FeatureVectorValues> tryFetch(
- Collection<DatasetReference> datasets, List<String> featureCodes,
- IScreeningBusinessObjectFactory businessObjectFactory)
- {
- assert datasets.size() > 0 : "No feature vector datasets specified.";
- return new FeatureVectorRetriever(businessObjectFactory, featureCodes)
- .tryFetch(datasets);
- }
-
- private final IScreeningBusinessObjectFactory businessObjectFactory;
-
- private final List<String> featureCodes;
-
- public FeatureVectorRetriever(IScreeningBusinessObjectFactory businessObjectFactory,
- List<String> featureCodes)
- {
- this.businessObjectFactory = businessObjectFactory;
- this.featureCodes = featureCodes;
- }
-
- private WellFeatureCollection<FeatureVectorValues> tryFetch(
- Collection<DatasetReference> datasets)
- {
- GroupByMap<String/* datastore code */, DatasetReference> datastoreToDatasetsMap =
- GroupByMap.create(datasets, new IKeyExtractor<String, DatasetReference>()
- {
- public String getKey(DatasetReference datasetReference)
- {
- return datasetReference.getDatastoreCode();
- }
- });
- WellFeatureCollection<FeatureVectorValues> allFeatures = null;
- for (String datastoreCode : datastoreToDatasetsMap.getKeys())
- {
- List<DatasetReference> datasetsForDatastore =
- datastoreToDatasetsMap.getOrDie(datastoreCode);
- WellFeatureCollection<FeatureVectorValues> features =
- fetchFromDatastore(datastoreCode, datasetsForDatastore);
- if (allFeatures == null)
- {
- allFeatures = features;
- } else
- {
- mergeFeatures(allFeatures, features);
- }
- }
- return allFeatures;
- }
-
- private static void mergeFeatures(WellFeatureCollection<FeatureVectorValues> allFeatures,
- WellFeatureCollection<FeatureVectorValues> features)
- {
- if (allFeatures.getFeatureCodes().equals(features.getFeatureCodes()) == false)
- {
- throw new IllegalStateException(
- "Cannot merge feature vectors from different datastores because the have different set of features: '"
- + allFeatures.getFeatureCodes()
- + "' and '"
- + features.getFeatureCodes() + "'.");
- }
- allFeatures.getFeatures().addAll(features.getFeatures());
- }
-
- private WellFeatureCollection<FeatureVectorValues> fetchFromDatastore(String datastoreCode,
- List<DatasetReference> datasets)
- {
- IHCSFeatureVectorLoader loader =
- businessObjectFactory.createHCSFeatureVectorLoader(datastoreCode);
- return loader.fetchDatasetFeatureValues(extractCodes(datasets), featureCodes);
- }
-
- private static List<String> extractCodes(List<DatasetReference> datasets)
- {
- return CollectionUtils.map(datasets,
- new ICollectionMappingFunction<String, DatasetReference>()
- {
- public String map(DatasetReference element)
- {
- return element.getCode();
- }
- });
- }
- }
-
- private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
- Set<PlateIdentifier> plates)
- {
- FeatureVectorDatasetLoader datasetsRetriever = createFeatureVectorDatasetsRetriever(plates);
- Collection<ExternalData> featureVectorDatasets =
- datasetsRetriever.getFeatureVectorDatasets();
- if (featureVectorDatasets.isEmpty())
- {
- return null;
- }
- List<DatasetReference> datasetPerPlate = chooseSingleDatasetForPlate(featureVectorDatasets);
- List<String> featureCodes = settings.getFeatureCodes();
- return FeatureVectorRetriever
- .tryFetch(datasetPerPlate, featureCodes, businessObjectFactory);
- }
-
private static Map<WellReference, FeatureVectorValues> createWellToFeatureVectorMap(
WellFeatureCollection<FeatureVectorValues> featureVectors)
{
@@ -496,35 +349,4 @@ public class ExperimentFeatureVectorSummaryLoader extends AbstractContentLoader
return wellToFeatureVectorMap;
}
- // TODO 2011-04-04, Tomasz Pylak: here if the plate has more than one dataset assigned, we
- // take the first and ignore the rest. The clean solution would be to introduce analysis
- // runs, where each plate has at most one analysis dataset in each run. {@link
- // UniqueKeyViolationStrategy} could be set to {@link UniqueKeyViolationStrategy.ERROR} in
- // such a case.
- protected static List<DatasetReference> chooseSingleDatasetForPlate(
- Collection<ExternalData> datasets)
- {
- TableMap<String, ExternalData> plateToDatasetMap =
- new TableMap<String, ExternalData>(datasets,
- new IKeyExtractor<String, ExternalData>()
- {
- public String getKey(ExternalData externalData)
- {
- Sample plate = externalData.getSample();
- return plate != null ? plate.getPermId() : null;
- }
- }, UniqueKeyViolationStrategy.KEEP_FIRST);
-
- List<DatasetReference> datasetPerPlate = new ArrayList<DatasetReference>();
- for (String platePermId : plateToDatasetMap.keySet())
- {
- if (platePermId != null)
- {
- ExternalData dataset = plateToDatasetMap.getOrDie(platePermId);
- DatasetReference datasetReference = ScreeningUtils.createDatasetReference(dataset);
- datasetPerPlate.add(datasetReference);
- }
- }
- return datasetPerPlate;
- }
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialAllAssaysFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialAllAssaysFeatureVectorSummaryLoader.java
new file mode 100644
index 0000000000000000000000000000000000000000..15789fed5d4c25cb29944fda1516a38e14c70152
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialAllAssaysFeatureVectorSummaryLoader.java
@@ -0,0 +1,203 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.collections.CollectionUtils.ICollectionMappingFunction;
+import ch.systemsx.cisd.common.collections.GroupByMap;
+import ch.systemsx.cisd.common.collections.IKeyExtractor;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorValues;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSimpleFeatureVectorSummary;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
+
+/**
+ * Finds all experiments where the given material is present and calculates summaries for feature
+ * vectors (if analysis data are available) .
+ *
+ * @author Tomasz Pylak
+ */
+public class MaterialAllAssaysFeatureVectorSummaryLoader extends AbstractContentLoader
+{
+ public static List<MaterialSimpleFeatureVectorSummary> loadMaterialFeatureVectorsFromAllAssays(
+ Session session, IScreeningBusinessObjectFactory businessObjectFactory,
+ IDAOFactory daoFactory, TechId materialId, MaterialSummarySettings settings)
+ {
+ List<WellContent> allAssayWellsForMaterial =
+ WellContentLoader.loadOnlyMetadata(session, businessObjectFactory, daoFactory,
+ materialId);
+ return new MaterialAllAssaysFeatureVectorSummaryLoader(session, businessObjectFactory,
+ daoFactory, settings).loadMaterialFeatureVectorsFromAllAssays(materialId,
+ allAssayWellsForMaterial);
+ }
+
+ private final MaterialSummarySettings settings;
+
+ private MaterialAllAssaysFeatureVectorSummaryLoader(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory,
+ MaterialSummarySettings settings)
+ {
+ super(session, businessObjectFactory, daoFactory);
+ this.settings = settings;
+ }
+
+ /**
+ * Note that different experiments can have different set of features!
+ */
+ private List<MaterialSimpleFeatureVectorSummary> loadMaterialFeatureVectorsFromAllAssays(
+ TechId materialId, List<WellContent> allAssayWellsForMaterial)
+ {
+ Set<PlateIdentifier> plates = extractPlates(allAssayWellsForMaterial);
+ WellFeatureCollection<FeatureVectorValues> allWellFeaturesOrNull =
+ tryLoadWellSingleFeatureVectors(plates);
+
+ Map<ExperimentReference, Set<WellReference>> wellsForExperimentMap =
+ groupWellsByExperiment(allAssayWellsForMaterial);
+
+ List<MaterialSimpleFeatureVectorSummary> summaries =
+ new ArrayList<MaterialSimpleFeatureVectorSummary>();
+ for (ExperimentReference experiment : wellsForExperimentMap.keySet())
+ {
+ Set<WellReference> experimentWells = wellsForExperimentMap.get(experiment);
+
+ MaterialSimpleFeatureVectorSummary summary =
+ calculateExperimentFeatureVectorSummary(materialId, experiment,
+ experimentWells, allWellFeaturesOrNull);
+ summaries.add(summary);
+ }
+ return summaries;
+ }
+
+ private MaterialSimpleFeatureVectorSummary calculateExperimentFeatureVectorSummary(
+ TechId materialId, ExperimentReference experiment, Set<WellReference> experimentWells,
+ WellFeatureCollection<FeatureVectorValues> allWellFeaturesOrNull)
+ {
+ if (allWellFeaturesOrNull == null)
+ {
+ return new MaterialSimpleFeatureVectorSummary(experiment);
+ }
+
+ List<IWellData> experimentWellData =
+ selectExperimentWellData(experimentWells, allWellFeaturesOrNull, materialId);
+ float[] summaryFeatureVector =
+ WellReplicaSummaryCalculator.calculateSummaryFeatureVector(experimentWellData,
+ settings.getAggregationType());
+ return new MaterialSimpleFeatureVectorSummary(experiment,
+ allWellFeaturesOrNull.getFeatureCodesAndLabels(), summaryFeatureVector);
+ }
+
+ private static List<IWellData> selectExperimentWellData(Set<WellReference> experimentWells,
+ WellFeatureCollection<FeatureVectorValues> allWellFeatures, TechId materialId)
+ {
+ List<String> orderedFeatureLabels = allWellFeatures.getFeatureLabels();
+
+ List<IWellData> experimentWellDataList = new ArrayList<IWellData>();
+ List<FeatureVectorValues> features = allWellFeatures.getFeatures();
+ for (FeatureVectorValues feature : features)
+ {
+ if (experimentWells.contains(feature.getWellReference()))
+ {
+ float[] values =
+ WellFeatureCollectionLoader.asFeatureVectorValues(feature,
+ orderedFeatureLabels);
+ IWellData wellData = new WellData(materialId.getId(), values);
+ experimentWellDataList.add(wellData);
+ }
+ }
+ return experimentWellDataList;
+ }
+
+ private static Map<ExperimentReference, Set<WellReference>> groupWellsByExperiment(
+ List<WellContent> allAssayWellsForMaterial)
+ {
+ GroupByMap<ExperimentReference, WellContent> expToWellContentMap =
+ GroupByMap.create(allAssayWellsForMaterial,
+ new IKeyExtractor<ExperimentReference, WellContent>()
+ {
+ public ExperimentReference getKey(WellContent wellContent)
+ {
+ return wellContent.getExperiment();
+ }
+ });
+ return convertToWellReferences(expToWellContentMap);
+ }
+
+ private static Map<ExperimentReference, Set<WellReference>> convertToWellReferences(
+ GroupByMap<ExperimentReference, WellContent> expToWellContentMap)
+ {
+ Map<ExperimentReference, Set<WellReference>> map =
+ new HashMap<ExperimentReference, Set<WellReference>>();
+ for (ExperimentReference exp : expToWellContentMap.getKeys())
+ {
+ List<WellContent> wellContents = expToWellContentMap.getOrDie(exp);
+ map.put(exp, asWellReferences(wellContents));
+ }
+ return map;
+ }
+
+ private static Set<WellReference> asWellReferences(List<WellContent> wellContents)
+ {
+ List<WellReference> wells =
+ CollectionUtils.map(wellContents,
+ new ICollectionMappingFunction<WellReference, WellContent>()
+ {
+ public WellReference map(WellContent wellContent)
+ {
+ return new WellReference(wellContent.tryGetLocation(),
+ wellContent.getPlate().getPermId());
+ }
+ });
+ return new HashSet<WellReference>(wells);
+ }
+
+ private static Set<PlateIdentifier> extractPlates(List<WellContent> wells)
+ {
+ Set<PlateIdentifier> plates = new HashSet<PlateIdentifier>();
+ for (WellContent well : wells)
+ {
+ String platePermId = well.getPlate().getPermId();
+ PlateIdentifier plateIdent = PlateIdentifier.createFromPermId(platePermId);
+ plates.add(plateIdent);
+ }
+ return plates;
+ }
+
+ private WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
+ Set<PlateIdentifier> plateIdentifiers)
+ {
+ return new WellFeatureCollectionLoader(session, businessObjectFactory, daoFactory)
+ .tryLoadWellSingleFeatureVectors(plateIdentifiers, settings.getFeatureCodes());
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
index 1430c9256d587e62553293aebfb617393e52ccd3..09604792a2df91c636d6f05963b172800dce9f79 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoader.java
@@ -43,9 +43,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialBiolog
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaFeatureSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaFeatureSummaryResult;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSimpleFeatureVectorSummary;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
-import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
/**
* For the specified material in the specified experiment loads feature vectors (details and
@@ -56,30 +54,6 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
*/
public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorSummaryLoader
{
- public static List<MaterialSimpleFeatureVectorSummary> loadMaterialFeatureVectorsFromAllAssays(
- Session session, IScreeningBusinessObjectFactory businessObjectFactory,
- IDAOFactory daoFactory, TechId materialId, MaterialSummarySettings settings)
- {
- List<WellContent> allAssayWellsForMaterial =
- WellContentLoader.loadOnlyMetadata(session, businessObjectFactory, daoFactory,
- materialId);
- // Probably the result DTO has to be converted (here?) to fit the GUI needs better.
- // Note that different experiments can have different set of features!
- return new MaterialFeatureVectorSummaryLoader(session, businessObjectFactory, daoFactory,
- settings).loadMaterialFeatureVectorsFromAllAssays(materialId,
- allAssayWellsForMaterial);
- }
-
- /**
- * Note that different experiments can have different set of features!
- */
- private List<MaterialSimpleFeatureVectorSummary> loadMaterialFeatureVectorsFromAllAssays(
- TechId materialId, List<WellContent> allAssayWellsForMaterial)
- {
- // TODO 2011-05-20, Tomasz Pylak: implement me!
- return null;
- }
-
/**
* For comments {@See MaterialFeatureVectorSummaryLoader}.
*/
@@ -286,7 +260,8 @@ public class MaterialFeatureVectorSummaryLoader extends ExperimentFeatureVectorS
List<? extends IWellData> experimentWellDataList)
{
List<MaterialIdFeatureVectorSummary> featureSummaries =
- calculateReplicasFeatureVectorSummaries(experimentWellDataList);
+ WellReplicaSummaryCalculator.calculateReplicasFeatureVectorSummaries(
+ experimentWellDataList, settings.getAggregationType());
return tryFindMaterialSummary(materialId, featureSummaries);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
new file mode 100644
index 0000000000000000000000000000000000000000..18c5fe2bce031389b194e8a6472dc22345bdf5b4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellFeatureCollectionLoader.java
@@ -0,0 +1,212 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import ch.systemsx.cisd.common.collections.CollectionUtils;
+import ch.systemsx.cisd.common.collections.CollectionUtils.ICollectionMappingFunction;
+import ch.systemsx.cisd.common.collections.GroupByMap;
+import ch.systemsx.cisd.common.collections.IKeyExtractor;
+import ch.systemsx.cisd.common.collections.TableMap;
+import ch.systemsx.cisd.common.collections.TableMap.UniqueKeyViolationStrategy;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
+import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureValue;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.FeatureVectorValues;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.FeatureVectorLoader.WellFeatureCollection;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSFeatureVectorLoader;
+
+/**
+ * Loads feature vectors for chosen plates.
+ *
+ * @author Tomasz Pylak
+ */
+public class WellFeatureCollectionLoader extends AbstractContentLoader
+{
+ public WellFeatureCollectionLoader(Session session,
+ IScreeningBusinessObjectFactory businessObjectFactory, IDAOFactory daoFactory)
+ {
+ super(session, businessObjectFactory, daoFactory);
+ }
+
+ /** Loads feature vectors for chosen plates and set of features */
+ public WellFeatureCollection<FeatureVectorValues> tryLoadWellSingleFeatureVectors(
+ Set<PlateIdentifier> plates, List<String> featureCodes)
+ {
+ FeatureVectorDatasetLoader datasetsRetriever = createFeatureVectorDatasetsRetriever(plates);
+ Collection<ExternalData> featureVectorDatasets =
+ datasetsRetriever.getFeatureVectorDatasets();
+ if (featureVectorDatasets.isEmpty())
+ {
+ return null;
+ }
+ List<DatasetReference> datasetPerPlate = chooseSingleDatasetForPlate(featureVectorDatasets);
+ return FeatureVectorRetriever
+ .tryFetch(datasetPerPlate, featureCodes, businessObjectFactory);
+ }
+
+ // TODO 2011-04-04, Tomasz Pylak: here if the plate has more than one dataset assigned, we
+ // take the first and ignore the rest. The clean solution would be to introduce analysis
+ // runs, where each plate has at most one analysis dataset in each run. {@link
+ // UniqueKeyViolationStrategy} could be set to {@link UniqueKeyViolationStrategy.ERROR} in
+ // such a case.
+ private static List<DatasetReference> chooseSingleDatasetForPlate(
+ Collection<ExternalData> datasets)
+ {
+ TableMap<String, ExternalData> plateToDatasetMap =
+ new TableMap<String, ExternalData>(datasets,
+ new IKeyExtractor<String, ExternalData>()
+ {
+ public String getKey(ExternalData externalData)
+ {
+ Sample plate = externalData.getSample();
+ return plate != null ? plate.getPermId() : null;
+ }
+ }, UniqueKeyViolationStrategy.KEEP_FIRST);
+
+ List<DatasetReference> datasetPerPlate = new ArrayList<DatasetReference>();
+ for (String platePermId : plateToDatasetMap.keySet())
+ {
+ if (platePermId != null)
+ {
+ ExternalData dataset = plateToDatasetMap.getOrDie(platePermId);
+ DatasetReference datasetReference = ScreeningUtils.createDatasetReference(dataset);
+ datasetPerPlate.add(datasetReference);
+ }
+ }
+ return datasetPerPlate;
+ }
+
+ /**
+ * Fetches feature vectors from different datastores and merges them (assuming that feature
+ * codes are the same).
+ */
+ private static class FeatureVectorRetriever
+ {
+ public static WellFeatureCollection<FeatureVectorValues> tryFetch(
+ Collection<DatasetReference> datasets, List<String> featureCodes,
+ IScreeningBusinessObjectFactory businessObjectFactory)
+ {
+ assert datasets.size() > 0 : "No feature vector datasets specified.";
+ return new FeatureVectorRetriever(businessObjectFactory, featureCodes)
+ .tryFetch(datasets);
+ }
+
+ private final IScreeningBusinessObjectFactory businessObjectFactory;
+
+ private final List<String> featureCodes;
+
+ public FeatureVectorRetriever(IScreeningBusinessObjectFactory businessObjectFactory,
+ List<String> featureCodes)
+ {
+ this.businessObjectFactory = businessObjectFactory;
+ this.featureCodes = featureCodes;
+ }
+
+ private WellFeatureCollection<FeatureVectorValues> tryFetch(
+ Collection<DatasetReference> datasets)
+ {
+ GroupByMap<String/* datastore code */, DatasetReference> datastoreToDatasetsMap =
+ GroupByMap.create(datasets, new IKeyExtractor<String, DatasetReference>()
+ {
+ public String getKey(DatasetReference datasetReference)
+ {
+ return datasetReference.getDatastoreCode();
+ }
+ });
+ WellFeatureCollection<FeatureVectorValues> allFeatures = null;
+ for (String datastoreCode : datastoreToDatasetsMap.getKeys())
+ {
+ List<DatasetReference> datasetsForDatastore =
+ datastoreToDatasetsMap.getOrDie(datastoreCode);
+ WellFeatureCollection<FeatureVectorValues> features =
+ fetchFromDatastore(datastoreCode, datasetsForDatastore);
+ if (allFeatures == null)
+ {
+ allFeatures = features;
+ } else
+ {
+ mergeFeatures(allFeatures, features);
+ }
+ }
+ return allFeatures;
+ }
+
+ private static void mergeFeatures(WellFeatureCollection<FeatureVectorValues> allFeatures,
+ WellFeatureCollection<FeatureVectorValues> features)
+ {
+ if (allFeatures.getFeatureCodes().equals(features.getFeatureCodes()) == false)
+ {
+ throw new IllegalStateException(
+ "Cannot merge feature vectors from different datastores because the have different set of features: '"
+ + allFeatures.getFeatureCodes()
+ + "' and '"
+ + features.getFeatureCodes() + "'.");
+ }
+ allFeatures.getFeatures().addAll(features.getFeatures());
+ }
+
+ private WellFeatureCollection<FeatureVectorValues> fetchFromDatastore(String datastoreCode,
+ List<DatasetReference> datasets)
+ {
+ IHCSFeatureVectorLoader loader =
+ businessObjectFactory.createHCSFeatureVectorLoader(datastoreCode);
+ return loader.fetchDatasetFeatureValues(extractCodes(datasets), featureCodes);
+ }
+
+ private static List<String> extractCodes(List<DatasetReference> datasets)
+ {
+ return CollectionUtils.map(datasets,
+ new ICollectionMappingFunction<String, DatasetReference>()
+ {
+ public String map(DatasetReference element)
+ {
+ return element.getCode();
+ }
+ });
+ }
+ }
+
+ public static float[] asFeatureVectorValues(FeatureVectorValues featureVector,
+ List<String> orderedFeatureLabels)
+ {
+ Map<String, FeatureValue> featureMap = featureVector.getFeatureMap();
+ float[] values = new float[featureMap.size()];
+ int i = 0;
+ for (String featureLabel : orderedFeatureLabels)
+ {
+ FeatureValue featureValue = featureMap.get(featureLabel);
+ values[i++] = asFloat(featureValue);
+ }
+ return values;
+ }
+
+ private static float asFloat(FeatureValue featureValue)
+ {
+ return featureValue.isFloat() ? featureValue.asFloat() : Float.NaN;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
index 877c98c50581c84218792d7a75c61360f52ba1b7..518f0d53227b3c7638b2f686eb609706490bce11 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculator.java
@@ -30,7 +30,7 @@ import ch.systemsx.cisd.common.collections.GroupByMap;
import ch.systemsx.cisd.common.collections.IKeyExtractor;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
/**
@@ -188,7 +188,7 @@ public class WellReplicaSummaryCalculator
{
Long replicaId = entry.getKey();
float[] aggregates = entry.getValue().getAggregates();
- IWellData summaryWellData = new WellData(replicaId, aggregates, null, null);
+ IWellData summaryWellData = new WellExtendedData(replicaId, aggregates, null, null);
summaryWellDataList.add(summaryWellData);
}
return summaryWellDataList;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellData.java
index faad1e050314296d1307c6ea2b3cfaeb081139df..3dc98d7fbd3b38c7a66dbb224679ca37982147a4 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellData.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellData.java
@@ -17,33 +17,22 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto;
import java.util.Arrays;
-import java.util.List;
-
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
/**
- * The simplest implementation of {@Link IWellExtendedData}.
+ * The simplest implementation of {@Link IWellData}.
*
* @author Tomasz Pylak
*/
-public class WellData implements IWellExtendedData
+public class WellData implements IWellData
{
private final long replicaId;
- private Sample well;
-
private final float[] featureVector;
- private final Material material;
-
- public WellData(long replicaId, float[] featureVector, Sample well, Material material)
+ public WellData(long replicaId, float[] featureVector)
{
- this.well = well;
this.featureVector = featureVector;
this.replicaId = replicaId;
- this.material = material;
}
public long getReplicaMaterialId()
@@ -51,35 +40,14 @@ public class WellData implements IWellExtendedData
return replicaId;
}
- public Sample getWell()
- {
- return well;
- }
-
public float[] getFeatureVector()
{
return featureVector;
}
- public Material getMaterial()
- {
- return material;
- }
-
@Override
public String toString()
{
return "repl " + replicaId + ": " + Arrays.toString(featureVector);
}
-
- public List<IEntityProperty> getProperties()
- {
- return well.getProperties();
- }
-
- public Long getId()
- {
- return well.getId();
- }
-
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellExtendedData.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellExtendedData.java
new file mode 100644
index 0000000000000000000000000000000000000000..32e62f85443b20d71f30ec1a19ea9745e96949d9
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellExtendedData.java
@@ -0,0 +1,63 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto;
+
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+
+/**
+ * The simplest implementation of {@Link IWellExtendedData}.
+ *
+ * @author Tomasz Pylak
+ */
+public class WellExtendedData extends WellData implements IWellExtendedData
+{
+ private Sample well;
+
+ private final Material material;
+
+ public WellExtendedData(long replicaId, float[] featureVector, Sample well, Material material)
+ {
+ super(replicaId, featureVector);
+ this.well = well;
+ this.material = material;
+ }
+
+ public Sample getWell()
+ {
+ return well;
+ }
+
+ public Material getMaterial()
+ {
+ return material;
+ }
+
+ public List<IEntityProperty> getProperties()
+ {
+ return well.getProperties();
+ }
+
+ public Long getId()
+ {
+ return well.getId();
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ExperimentReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ExperimentReference.java
index 2e98b79183291e89803629d71d682eb2226188ba..6473e4f7b5e1cc07e7f0e277068e6557acdb44cd 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ExperimentReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ExperimentReference.java
@@ -107,4 +107,29 @@ public class ExperimentReference implements ISerializable, IEntityInformationHol
{
return getIdentifier();
}
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + (int) (experimentId ^ (experimentId >>> 32));
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ return true;
+ if (obj == null)
+ return false;
+ if (getClass() != obj.getClass())
+ return false;
+ ExperimentReference other = (ExperimentReference) obj;
+ if (experimentId != other.experimentId)
+ return false;
+ return true;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSimpleFeatureVectorSummary.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSimpleFeatureVectorSummary.java
index ba74534835193d5f92c8558414786fbb02fd8496..f9094b78fd7c58fe0816b7533c94264b3cd456b9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSimpleFeatureVectorSummary.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/MaterialSimpleFeatureVectorSummary.java
@@ -16,11 +16,12 @@
package ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto;
+import java.util.ArrayList;
import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.basic.ISerializable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.CodeAndLabel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ExperimentReference;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ServiceVersionHolder;
/**
@@ -32,21 +33,30 @@ public class MaterialSimpleFeatureVectorSummary implements ISerializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
- private Experiment experiment;
+ private ExperimentReference experiment;
- // has the same length as feature vectors summary
+ // Has the same length as feature vectors summary.
+ // Note that it can be empty if there are no analysis results!
private List<CodeAndLabel> featureDescriptions;
private float[] featureVectorSummary;
// GTW
- // TODO KE: create a separate DTO for the UI layer if there is enough time
@SuppressWarnings("unused")
private MaterialSimpleFeatureVectorSummary()
{
}
- public MaterialSimpleFeatureVectorSummary(Experiment experiment,
+ /**
+ * Useful when there are no analysis results for a material in the experiment (but there can be
+ * still some images acquired).
+ */
+ public MaterialSimpleFeatureVectorSummary(ExperimentReference experiment)
+ {
+ this(experiment, new ArrayList<CodeAndLabel>(), new float[0]);
+ }
+
+ public MaterialSimpleFeatureVectorSummary(ExperimentReference experiment,
List<CodeAndLabel> featureDescriptions, float[] featureVectorSummary)
{
this.experiment = experiment;
@@ -54,7 +64,7 @@ public class MaterialSimpleFeatureVectorSummary implements ISerializable
this.featureVectorSummary = featureVectorSummary;
}
- public Experiment getExperiment()
+ public ExperimentReference getExperiment()
{
return experiment;
}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
index c9fefa41a60c69f011c7c7f65f7e57093678dfc4..2a6db8a96558385d63bcc1afe8d5b7169c3f9036 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/MaterialFeatureVectorSummaryLoaderTest.java
@@ -39,7 +39,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellExtendedD
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialAllReplicasFeatureVectors;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialBiologicalReplicateFeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellDataCollection;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialSummarySettings;
@@ -147,6 +147,6 @@ public class MaterialFeatureVectorSummaryLoaderTest extends AssertJUnit
material.setProperties(properties);
well.setProperties(properties);
- return new WellData(replicaId, featureValues, well, material);
+ return new WellExtendedData(replicaId, featureValues, well, material);
}
}
\ No newline at end of file
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
index 69f2f5322fc4d09d5bc49ca3926ebdc732746840..739e1be813f4bce3e7726cbb24d0bbf8b7eddfc7 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/WellReplicaSummaryCalculatorTest.java
@@ -33,7 +33,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Material;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellReplicaSummaryCalculator.SummaryFeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.IWellData;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.MaterialIdFeatureVectorSummary;
-import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellData;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellExtendedData;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.MaterialReplicaSummaryAggregationType;
/**
@@ -206,7 +206,7 @@ public class WellReplicaSummaryCalculatorTest extends AssertJUnit
{
Material material = new Material();
material.setId(replicaId);
- return new WellData(replicaId, featureValues, null, material);
+ return new WellExtendedData(replicaId, featureValues, null, material);
}
private List<MaterialIdFeatureVectorSummary> calculate(List<IWellData> wellDataList)